Thermosensitive, extracellular neutral proteases in Bacillus subtilis: isolation, characterization, and genetics.

Two mutants (NT02 and NT17), each producing a thermosensitive neutral protease, were isolated from Bacillus subtilis NP58, a transformant which acquired the property of hyperproduction of neutral protease from Bacillus natto IAM 1212. The neutral proteases produced by these two mutants were partially purified and enzymologically characterized. The two mutant neutral proteases displayed increased thermosensitivity as well as altered pH optima compared with those of the NP58 enzyme. In addition, the hydrolytic activity of the thermosensitive neutral proteases on synthetic peptide substrates was found to be extremely different. These results strongly suggest that the site of mutation in each of the temperature-sensitive strains is located within the structural gene for neutral protease (nprE). Previous studies indicated the existence of a specific regulator gene (nprR) in addition to the structural gene for neutral protease. Phage PBS1-mediated transduction and deoxyribonucleic acid-mediated transformation studies with the parental and mutant strains suggest that the chromosomal order of these genes is recA-pyrA-nprR-nprE-fruB-metC. Moreover, the results of these genetic analyses imply that the mutations to thermosensitivity are located proximate to each other within the nprE gene.     

Robustness, evolvability, and neutrality

Biological systems, from macromolecules to whole organisms, are robust if they continue to function, survive, or reproduce when faced with mutations, environmental change, and internal noise. I focus here on biological systems that are robust to mutations and ask whether such systems are more or less evolvable, in the sense that they can acquire novel properties. The more robust a system is, the more mutations in it are neutral, that is, without phenotypic effect. I argue here that such neutral change--and thus robustness--can be a key to future evolutionary innovation, if one accepts that neutrality is not an essential feature of a mutation. That is, a once neutral mutation may cause phenotypic effects in a changed environment or genetic background. I argue that most, if not all, neutral mutations are of this sort, and that the essentialist notion of neutrality should be abandoned. This perspective reconciles two opposing views on the forces dominating organismal evolution, natural selection and random drift: neutral mutations occur and are especially abundant in robust systems, but they do not remain neutral indefinitely, and eventually become visible to natural selection, where some of them lead to evolutionary innovations.     

Connectivity of Neutral Networks,Overdispersion, and Structural Conservation in Protein Evolution

Abstract Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds, determining that an extended neutral network in sequence space is associated with each of them. Within our model, neutral evolution leads to a non-Poissonian substitution process, due to the broad distribution of connectivities in neutral networks. The observation that the substitution process has non-Poissonian statistics has been used to argue against the original Kimura neutral theory, while our model shows that this is a generic property of neutral evolution with structural conservation. Our model also predicts that the substitution rate can strongly fluctuate from one branch to another of the evolutionary tree. The average sequence similarity within a neutral network is close to the threshold of randomness, as observed for families of sequences sharing the same fold. Nevertheless, some positions are more difficult to mutate than others. We compare such structurally conserved positions to positions conserved in protein evolution, suggesting that our model can be a valuable tool to distinguish structural from functional conservation in databases of protein families. These results indicate that a synergy between database analysis and structurally based computational studies can increase our understanding of protein evolution.     

Human hemoglobin: polymorphism, neutrality of variants, evolutionary aspect

Integrated analysis of the polymorphism of human hemoglobin has been made using populational genetics, hematological, physiological, protein chemistry and molecular biology data. The known variants of human hemoglobin are conventionally classified as "widely common", "less common" and "rare", depending on their contribution to polymorphism. The importance of homeostasis and compensatory reactions for maintaining the resistance of the human body against mutant hemoglobins is emphasized. Hb D Punjab and Hb O Arab being relatively neutral, the genetic structure of populations may restrict their distribution. A hypothesis is put forward concerning the possible role of an increased local conformational mobility of protein in creating neutral protein variants. It is proposed to discriminate between truly neutral and pseudoneutral protein variants. In case of possible changes in the genetic and environmental factors, the former are not subject to selection, while the latter may be. Contribution to neutral evolution can be made only by truly neutral variants. In a compensated heterozygotic state the truly neutral and pseudoneutral variants may give rise to new functions and adaptively valuable properties in protein. The evolution of proteins is believed to proceed from a stage which is consistent with M. Kimura's concept of neutrality of protein polymorphism toward a stage which is consistent with the concept of selectionism. It is concluded, that the currently observed degree of polymorphism of human hemoglobin corresponds to the present stage of molecular evolution of the protein.     

Immigration,Local Dispersal Limitation,and the Repeatability of Community Composition under Neutral and Niche Dynamics

Repeatability of community composition has been a critical aspect for community structure, which is closely associated with community stability, predictability, conservation biology and ecological restoration. It has been shown that both immigration and local dispersal limitation can affect the community composition in both neutral and niche model. Hence, we use a spatially explicit individual-based model to investigate the potential influence of immigration rate and strength of local dispersal limitation on repeatability in both neutral and niche models. Similarity measures are used to quantify repeatability. We examine the repeatability of community composition among replicate communities (which means the same community repeats many times), and between niche and neutral replicate communities. We find the correlation between repeatability and immigration rate is positive in the neutral model and an inverted unimodal in the niche model. The correlation between repeatability and local dispersal distance is positive in the niche model and negative in the neutral model. High repeatability between niche communities and neutral communities is observed with high immigration rates or when high local dispersal distance appears in the niche model or low local dispersal distance in the neutral model. Our results show that repeatability of community composition is not only dependent on the types of community models (niche vs. neutrality) but also strongly determined by immigration rates and local dispersal limitation.     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

Cloning, sequencing and expression of the gene encoding the extracellular neutral protease, vibriolysin, of Vibrio proteolyticus.

The gene (nprV), encoding the extracellular neutral protease, vibriolysin (NprV), of the Gram- marine microorganism, Vibrio proteolyticus, was isolated from a V. proteolyticus DNA library constructed in Escherichia coli. The recombinant E. coli produced a protease that co-migrated with purified neutral protease from V. proteolyticus on non-denaturing polyacrylamide gels, and that demonstrated enzymatic specificity towards the neutral protease substrate N-[3-(2-furyl)acryloyl]-L-alanylphenylalanine amide. The nucleotide (nt) sequence of the cloned nprV gene revealed an open reading frame encoding 609 amino acids (aa) including a putative signal peptide sequence followed by a long 'pro' sequence consisting of 172 aa. The N-terminal aa sequence of NprV purified from cultures of V. proteolyticus, identified the beginning of the mature protein within the aa sequence deduced from the nt sequence. Comparative analysis of mature NprV to the sequences of the neutral proteases from Bacillus thermoproteolyticus (thermolysin) and Bacillus stearothermophilus identified extensive regions of conserved aa homology, particularly with respect to active-site residues, zinc-binding residues, and calcium-binding sites. NprV was overproduced in Bacillus subtilis by placing the DNA encoding the 'pro' and mature enzyme downstream from a Bacillus promoter and signal sequence.     

Subcellular distribution of acid and neutral alpha-glucosidases in normal, acid maltase deficient, and myophosphorylase deficient human skeletal muscle

The subcellular distribution of acid (pH 4.0) and neutral (pH 6.5) α-glucosidases was investigated in biopsy specimens of human skeletal muscle obtained from six normal subjects, four adult cases of acid maltase deficiency, and a case of myophosphorylase deficiency. The highest relative specific activity of acid glucosidase, as well as of other acid hydrolases, was observed in the light mitochondrial fraction. Relatively high acid phosphatase activity was also found in the microsomal fraction. In all muscles the highest relative specific activity of neutral glucosidase was in the microsomal fraction. In acid glucosidase deficient muscle no neutral glucosidase could be detected in the light and heavy mitochondrial fractions but in normal and myophosphorylase deficient muscle neutral glucosidase activity was also detectable in these fractions. The final supernatant of all muscles contained neutral glucoamylase activity. The relevance of these data to the pathogenesis of the different forms of type II glycogenosis is considered.     

Biochemical studies on an acidophilic, thermophilic bacterium, Bacillus acidocaldarius: isolation of bacteria, intracellular pH, and stabilities of biopolymers.

Acidophilic, thermophilic bacteria were isolated from Japanese acidic hot springs. They were spore-forming rods, identified as Bacillus acidocaldarius. DNA extracted from these acido-thermophiles showed no abnormality in chemical structure; it was instantly denatured and gradually decomposed giving rise to apurinic acid in a hot acid environment milder than the optimal conditions for the growth of the acido-thermophiles. Glyceraldehyde-3-phosphate dehydrogenase extracted from B. acidocaldarius was not active at pH 5 or less, and was resistant to heat at neutral but not acid pH. The intracellular pH was computed to be neutral by using dimethyl-2,4-oxazolidinedione. When uncouplers or inhibitors of respiration were added to the cells suspended in hot acid solution, the estimated pH was not changed and glyceraldehyde-3-phosphate dehydrogenase in the cells was not denatured. These results suggest that the cytoplasm of B. acidocaldarius is a hot neutral environment, and that a pH gradient across the cell envelope can be maintained even when oxidative phosphorylation or respiration is inhibited.     

New insight into the structure,reaction mechanism,and biological functions of neutral ceramidase

Ceramidase (CDase) is an enzyme that hydrolyzes the N-acyl linkage between the sphingoid base and fatty acid of ceramide. These enzymes are classified into three distinct groups, acid (Asah1), neutral (Asah2), and alkaline (Asah3) CDases, based on their primary structure and optimum pH. Acid CDase catabolizes ceramide in lysosomes and is found only in vertebrates. In contrast, the distribution of neutral and alkaline CDases is broad, with both being found in species ranging from lower eukaryotes to mammals; however, only neutral CDase is found in prokaryotes, including some pathogenic bacteria. Neutral CDase is thought to have gained a specific domain (mucin box) in the N-terminal region after the vertebrate split, allowing the enzyme to be stably expressed at the plasma membrane as a type II membrane protein. The X-ray crystal structure of neutral CDase was recently solved, uncovering a unique structure and reaction mechanism for the enzyme. Neutral CDase contains a zinc ion in the active site that functions as a catalytic center, and the hydrolysis of the N-acyl linkage in ceramide proceeds through a mechanism that is similar to that described for zinc-dependent carboxypeptidase. This review describes the structure, reaction mechanism, and biological functions of neutral CDase in association with the molecular evolution, topology, and mechanical conformation. This article is part of a Special Issue entitled New Frontiers in Sphingolipid Biology.     

Heterologous gene expression in Lactococcus lactis subsp. lactis: synthesis, secretion, and processing of the Bacillus subtilis neutral protease

The Bacillus subtilis nprE gene lacking its own promoter sequence was inserted in the lactococcal expression vector pMG36e. Upon introduction of the recombinant plasmid into Lactococcus lactis subsp. lactis strain MG1363, neutral protease activity could be visualized by the appearance of large clearing zones around colonies grown on milk agar plates. By measuring the activities of the neutral protease and the intracellular enzyme lactate dehydrogenase in culture supernatants and cell fractions, it was demonstrated that the neutral protease was actively secreted into the growth medium. This was corroborated by using the Western blot (immunoblot) technique, which showed the presence of the mature form of the neutral protease in the culture supernatant. On the basis of these results, it is concluded that the B. subtilis neutral protease gene was expressed in L. lactis and that the gene product was secreted into the growth medium and was apparently correctly processed to produced a biologically active protein. The secretion of this particular enzyme may be helpful in achieving accelerated cheese ripening.     

Mass spectrometric analysis of neutral sphingolipids: methods, applications, and limitations

Sphingolipids represent an important class among lipids, especially when considering their vital roles in lipid metabolism. Thus, a variety of methods have been created to accomplish their analysis and the term "sphingolipidomics" has recently been coined to underline the motivation to enable a comprehensive analysis of all sphingolipid species including the acidic and the neutral ones. In this review, we summarize selected mainly biomedical based mass spectrometric approaches for the analysis of neutral sphingolipids regarding their advantages, applications and limitations. To underline some practical aspects of method development, we focus on a new method recently developed in our laboratory, which enables separation, detection, and mass spectrometric profiling of ceramide, hexosylceramide, lactosylceramide, globotriaosylceramide, globotetraosylceramide, sphingomyelin species, and cholesterol in one run. This method can be applied to investigate impairments of neutral sphingolipid metabolism in a variety of disorders such as sphingolipidoses and be employed to screen for sphingolipid profile changes as induced by knockout experiments or related studies.     

综论稻田生态系中性昆虫的意义及其调控

１　中性昆虫的概念及田间动态１．１　概念的提出吴进才等在对稻田节肢动物群落营养物种的系统调查中发现,稻田生态系中,既非害虫又非天敌的一类昆虫占整个节肢动物群落丰盛度的２０％～６５％［７,８］。生态学理论认为,系统中没有孤立存在的物种［１２］。数量庞大的这一昆虫类群在稻田生态系统中有何意义？与稻田害虫的发生有何联系？现有文献还少有涉及。吴进才等［７］、郭玉杰等［１］提出了中性昆虫的概念,用于指称传统植物保护学中的既非害虫又非天敌的一类昆虫,并就其田间动态及在食物网中的作用进行了系统调查、研究和讨论…     

Immunochemical studies of the combining sites of the two isolectins, A4 and B4, isolated from Bandeiraea simplicifolia

The tissue distribution and the effects of starvation and streptozotocin-induced diabetes on insulin B chain-degrading neutral peptidase activity in the rat have been studied. The neutral peptidase activity in tissue extracts was determined by measuring the formation of trichloroacetic acid-soluble radioactivity from ¹²⁵I-labeled B chain of insulin in 0.1 m Tris buffer (pH 7.2). Inhibition by several different compounds (EDTA, dithiothreitol, and potassium phosphate) which are known to inhibit the purified enzyme and the effects of pH suggest that the B chain-degrading activity measured in each of 12 tissue extracts may be similar to the neutral peptidase recently purified from rat kidney (P. T. Varandani and L. A. Shroyer, 1977, Arch. Biochem. Biophys., 181, 82–93). Neutral peptidase activity was observed in all tissues examined and varied in the order kidney ? intestine > pancreas, testis > liver > thymus > heart, skeletal muscle, diaphragm > lung, spleen > fat. Neutral peptidase activity in kidney, liver, fat, and skeletal muscle from diabetic animals was significantly depressed when compared with the levels in these tissues from normal animals. Insulin treatment of diabetic animals raised the neutral peptidase activity in kidney, liver, and fat to levels equivalent to or even exceeding normal levels; however, activity in skeletal muscle persisted at depressed levels. Heart muscle neutral peptidase activity was not significantly affected in either diabetes or starvation. In the liver, starvation reduced the level of neutral peptidase activity while subsequent refeeding raised the activity to a level exceeding the control. Opposite effects were observed in kidney: starvation increased neutral peptidase activity while refeeding brought the activity back to normal levels. Only small decreases in neutral peptidase activity were observed in fat and skeletal muscle after 24 h starvation, but were not evident after 64 h starvation. The changes in neutral peptidase activity correlated well with the changes in glutathione-insulin transhydrogenase activity previously reported in liver and kidney.     

New, highly efficient formulation of diclofenac for the topical, transdermal administration in ultradeformable drug carriers, Transfersomes

Unmodified and polyethylene glycol (PEG) modified neutral and negatively charged liposomes were prepared by freeze-thaw and extrusion followed by chromatographic purification. The effects of PEG molecular weight (PEG 550, 2000, 5000), PEG loading (0-15 mol%), and liposome surface charge on fibrinogen adsorption were quantified using radiolabeling techniques. All adsorption isotherms increased monotonically over the concentration range 0-3 mg/ml and adsorption levels were low. Negatively charged liposomes adsorbed significantly more fibrinogen than neutral liposomes. PEG modification had no effect on fibrinogen adsorption to neutral liposomes. An inverse relationship was found between PEG loading of negatively charged liposomes and fibrinogen adsorption. PEGs of all three molecular weights at a loading of 5 mol% reduced fibrinogen adsorption to negatively charged liposomes. Protein adsorption from diluted plasma (10% normal strength) to four different liposome types (neutral, PEG-neutral, negatively charged, and PEG-negatively charged) was investigated using gel electrophoresis and immunoblotting. The profiles of adsorbed proteins were similar on all four liposome types, but distinctly different from the profile of plasma itself, indicating a partitioning effect of the lipid surfaces. alpha2-macroglobulin and fibronectin were significantly enriched on the liposomes whereas albumin, transferrin, and fibrinogen were depleted compared to plasma. Apolipoprotein AI was a major component of the adsorbed protein layers. The blot of complement protein C3 adsorbed on the liposomes suggested that the complement system was activated.     

Heterologous gene expression in Lactococcus lactis subsp. lactis: synthesis, secretion, and processing of the Bacillus subtilis neutral protease.

The Bacillus subtilis nprE gene lacking its own promoter sequence was inserted in the lactococcal expression vector pMG36e. Upon introduction of the recombinant plasmid into Lactococcus lactis subsp. lactis strain MG1363, neutral protease activity could be visualized by the appearance of large clearing zones around colonies grown on milk agar plates. By measuring the activities of the neutral protease and the intracellular enzyme lactate dehydrogenase in culture supernatants and cell fractions, it was demonstrated that the neutral protease was actively secreted into the growth medium. This was corroborated by using the Western blot (immunoblot) technique, which showed the presence of the mature form of the neutral protease in the culture supernatant. On the basis of these results, it is concluded that the B. subtilis neutral protease gene was expressed in L. lactis and that the gene product was secreted into the growth medium and was apparently correctly processed to produced a biologically active protein. The secretion of this particular enzyme may be helpful in achieving accelerated cheese ripening.     

Swearing, euphemisms, and linguistic relativity

Participants read aloud swear words, euphemisms of the swear words, and neutral stimuli while their autonomic activity was measured by electrodermal activity. The key finding was that autonomic responses to swear words were larger than to euphemisms and neutral stimuli. It is argued that the heightened response to swear words reflects a form of verbal conditioning in which the phonological form of the word is directly associated with an affective response. Euphemisms are effective because they replace the trigger (the offending word form) by another word form that expresses a similar idea. That is, word forms exert some control on affect and cognition in turn. We relate these findings to the linguistic relativity hypothesis, and suggest a simple mechanistic account of how language may influence thinking in this context.     

长白山不同海拔梯度森林土壤中性糖分布特征

2010年7月,采集长白山北坡5个典型植被带(阔叶红松林、明针叶林、暗针叶林、岳桦林和高山苔原)林下土壤,研究了不同海拔梯度下森林土壤的中性单糖分布、数量及其影响因素,并结合中性糖来源差异探讨土壤有机质的生物化学积累机制.结果表明: 在长白山不同海拔梯度下,森林土壤的中性糖差异显著,中性糖来源碳在土壤有机碳(SOC)中的相对含量为80.55～170.63 mg·g^-1,并且随海拔升高呈递增的趋势.采用多元线性拟合分析发现,生长季平均气温是影响土壤中性糖相对含量的主要因素,低温有助于中性糖的积累.土壤中(半乳糖+甘露糖)/(阿拉伯糖+木糖)为1.62～2.28,且随海拔升高呈增加趋势,说明土壤中微生物来源中性糖的贡献随海拔升高逐渐增加.微生物熵随海拔升高而降低,说明低温条件下微生物活性下降而对外源碳的利用效率提高,植物残体被微生物分解转化后,以微生物同化物的形式固存于土壤中,从而增加了微生物来源中性糖的比例.     

Plasticity, evolvability, and modularity in RNA

RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype-phenotype map in which concepts like plasticity, evolvability, epistasis, and modularity can not only be precisely defined and statistically measured but also reveal simultaneous and profoundly non-independent effects of natural selection. Molecular plasticity is viewed here as the capacity of an RNA sequence to assume a variety of energetically favorable shapes by equilibrating among them at constant temperature. Through simulations based on experimental designs, we study the dynamics of a population of RNA molecules that evolve toward a predefined target shape in a constant environment. Each shape in the plastic repertoire of a sequence contributes to the overall fitness of the sequence in proportion to the time the sequence spends in that shape. Plasticity is costly, since the more shapes a sequence can assume, the less time it spends in any one of them. Unsurprisingly, selection leads to a reduction of plasticity (environmental canalization). The most striking observation, however, is the simultaneous slow-down and eventual halting of the evolutionary process. The reduction of plasticity entails genetic canalization, that is, a dramatic loss of variability (and hence a loss of evolvability) to the point of lock-in. The causal bridge between environmental canalization and genetic canalization is provided by a correlation between the set of shapes in the plastic repertoire of a sequence and the set of dominant (minimum free energy) shapes in its genetic neighborhood. This statistical property of the RNA genotype-phenotype map, which we call plastogenetic congruence, traps populations in regions where most genetic variation is phenotypically neutral. We call this phenomenon neutral confinement. Analytical models of neutral confinement, made tractable by the assumption of perfect plastogenetic congruence, formally connect mutation rate, the topography of phenotype space, and evolvability. These models identify three mutational regimes: that corresponding to neutral confinement, an exploration threshold corresponding to a breakdown of neutral confinement with the simultaneous persistence of the dominant phenotype, and a classic error threshold corresponding to the loss of the dominant phenotype. In a final step, we analyze the structural properties of canalized phenotypes. The reduction of plasticity leads to extreme modularity, which we analyze from several perspectives: thermophysical (melting--the RNA version of a norm of reaction), kinetic (folding pathways--the RNA version of development), and genetic (transposability--the insensitivity to genetic context). The model thereby suggests a possible evolutionary origin of modularity as a side effect of environmental canalization.     

The nearly neutral and selection theories of molecular evolution under the fisher geometrical framework: substitution rate, population size, and complexity

The general theories of molecular evolution depend on relatively arbitrary assumptions about the relative distribution and rate of advantageous, deleterious, neutral, and nearly neutral mutations. The Fisher geometrical model (FGM) has been used to make distributions of mutations biologically interpretable. We explored an FGM-based molecular model to represent molecular evolutionary processes typically studied by nearly neutral and selection models, but in which distributions and relative rates of mutations with different selection coefficients are a consequence of biologically interpretable parameters, such as the average size of the phenotypic effect of mutations and the number of traits (complexity) of organisms. A variant of the FGM-based model that we called the static regime (SR) represents evolution as a nearly neutral process in which substitution rates are determined by a dynamic substitution process in which the population's phenotype remains around a suboptimum equilibrium fitness produced by a balance between slightly deleterious and slightly advantageous compensatory substitutions. As in previous nearly neutral models, the SR predicts a negative relationship between molecular evolutionary rate and population size; however, SR does not have the unrealistic properties of previous nearly neutral models such as the narrow window of selection strengths in which they work. In addition, the SR suggests that compensatory mutations cannot explain the high rate of fixations driven by positive selection currently found in DNA sequences, contrary to what has been previously suggested. We also developed a generalization of SR in which the optimum phenotype can change stochastically due to environmental or physiological shifts, which we called the variable regime (VR). VR models evolution as an interplay between adaptive processes and nearly neutral steady-state processes. When strong environmental fluctuations are incorporated, the process becomes a selection model in which evolutionary rate does not depend on population size, but is critically dependent on the complexity of organisms and mutation size. For SR as well as VR we found that key parameters of molecular evolution are linked by biological factors, and we showed that they cannot be fixed independently by arbitrary criteria, as has usually been assumed in previous molecular evolutionary models.